NP-MRD: Showing NP-Card for Bergamotene D (NP0333698)

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Record Information

Version

2.0

Created at

2024-08-06 07:56:07 UTC

Updated at

2025-06-12 01:07:57 UTC

NP-MRD ID

NP0333698

Natural Product DOI

https://doi.org/10.57994/3177

Secondary Accession Numbers

None

Natural Product Identification

Common Name

Bergamotene D

Description

Bergamotene D belongs to the class of organic compounds known as branched fatty acids. These are fatty acids containing a branched chain. Based on a literature review very few articles have been published on Bergamotene D.

Structure

MOL SDF PDB SMILES InChI


  Mrv2104 04202310292D          

 18 18  0  0  1  0            999 V2000
    0.9959    1.5792    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125    0.9959    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.1709    1.5792    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0427    2.3761    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5407    2.9595    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3376    2.7460    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5511    1.9491    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9210    3.3293    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.9959    0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.8209    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2334   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2334    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.4125   -0.1709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1709    0.4125    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.9959    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4084    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2334    1.1270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9959    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  1  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  2  9  1  0  0  0  0
  9 10  1  6  0  0  0
 10 11  1  0  0  0  0
 10 12  2  0  0  0  0
  9 13  1  0  0  0  0
 14 13  1  0  0  0  0
  2 14  1  0  0  0  0
 14 15  1  6  0  0  0
 15 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 18  2  0  0  0  0
M  END
> <DATABASE_ID>
NP0333698

> <DATABASE_NAME>
NP-MRD

> <SMILES>
CC(C)=CCC[C@]1(C)[C@@H](CC(O)=O)C[C@H]1C(C)=O

> <INCHI_IDENTIFIER>
InChI=1S/C15H24O3/c1-10(2)6-5-7-15(4)12(9-14(17)18)8-13(15)11(3)16/h6,12-13H,5,7-9H2,1-4H3,(H,17,18)/t12-,13+,15-/m1/s1

> <INCHI_KEY>
ABKOZKISOSHHJC-VNHYZAJKSA-N

> <FORMULA>
C15H24O3

> <MOLECULAR_WEIGHT>
252.354

> <EXACT_MASS>
252.172544633

> <JCHEM_ACCEPTOR_COUNT>
3

> <JCHEM_ATOM_COUNT>
42

> <JCHEM_AVERAGE_POLARIZABILITY>
29.222732795732902

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-[(1R,2R,3R)-3-acetyl-2-methyl-2-(4-methylpent-3-en-1-yl)cyclobutyl]acetic acid

> <JCHEM_LOGP>
2.988771183666666

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
19.400010636889615

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.8605857857156245

> <JCHEM_PKA_STRONGEST_BASIC>
-7.3573541321715785

> <JCHEM_POLAR_SURFACE_AREA>
54.37

> <JCHEM_REFRACTIVITY>
71.8363

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
[(1R,2R,3R)-3-acetyl-2-methyl-2-(4-methylpent-3-en-1-yl)cyclobutyl]acetic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 20-APR-23   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   20-APR-23         0                                  
HETATM    1  C   UNK     0       1.859   2.948   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.770   1.859   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.319   2.948   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.080   4.435   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -1.009   5.524   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.497   5.126   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      -2.895   3.638   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -3.586   6.215   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       1.859   0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       3.399   0.770   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       4.169  -0.564   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       4.169   2.104   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       0.770  -0.319   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -0.319   0.770   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -1.859   0.770   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -2.629   2.104   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      -4.169   2.104   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      -1.859   3.437   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    9   14                                             
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    2   10   13                                                  
CONECT   10    9   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10                                                            
CONECT   13    9   14                                                       
CONECT   14   13    2   15                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17   18                                                  
CONECT   17   16                                                            
CONECT   18   16                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   36    0
END

View in JSmol

Synonyms

Not Available

Chemical Formula

C₁₅H₂₄O₃

Average Mass

252.3540 Da

Monoisotopic Mass

252.17254 Da

IUPAC Name

2-[(1R,2R,3R)-3-acetyl-2-methyl-2-(4-methylpent-3-en-1-yl)cyclobutyl]acetic acid

Traditional Name

[(1R,2R,3R)-3-acetyl-2-methyl-2-(4-methylpent-3-en-1-yl)cyclobutyl]acetic acid

CAS Registry Number

Not Available

SMILES

CC(C)=CCC[C@]1(C)[C@@H](CC(O)=O)C[C@H]1C(C)=O

InChI Identifier

InChI=1S/C15H24O3/c1-10(2)6-5-7-15(4)12(9-14(17)18)8-13(15)11(3)16/h6,12-13H,5,7-9H2,1-4H3,(H,17,18)/t12-,13+,15-/m1/s1

InChI Key

ABKOZKISOSHHJC-VNHYZAJKSA-N

Experimental Spectra

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
NOESY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	yangwc6@mail2.sysu.edu.cn	Sun Yat-sen university	Wencong Yang	2024-08-06	View Spectrum
HSQC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	yangwc6@mail2.sysu.edu.cn	Sun Yat-sen university	Wencong Yang	2024-08-06	View Spectrum
COSY NMR	[¹H, ¹H] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	yangwc6@mail2.sysu.edu.cn	Sun Yat-sen university	Wencong Yang	2024-08-06	View Spectrum
HMBC NMR	[¹H, ¹³C] NMR Spectrum (2D, 500 MHz, CD3OD, experimental)	yangwc6@mail2.sysu.edu.cn	Sun Yat-sen university	Wencong Yang	2024-08-06	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, CD3OD, experimental)	yangwc6@mail2.sysu.edu.cn	Sun Yat-sen university	Wencong Yang	2024-08-06	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 101 MHz, CD3OD, experimental)	yangwc6@mail2.sysu.edu.cn	Sun Yat-sen university	Wencong Yang	2024-08-06	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400.132470802 MHz, CD₃OD, experimental)	Wishart Lab	Wishart Lab	David Wishart	2021-06-20	View Spectrum

Predicted Spectra

Spectrum Type	Description	Depositor ID	Depositor Organization	Depositor	Deposition Date	View

Chemical Shift Submissions

Spectrum Type	Description	Depositor Email	Depositor Organization	Depositor	Deposition Date	View
1D NMR	¹H NMR Spectrum (1D, 400.132470802, CD₃OD, simulated)	yangwc6@mail2.sysu.edu.cn	Sun Yat-sen university	Wencong Yang	2024-08-06	View Spectrum

Species

Species of Origin

Species Name	Source	Reference
Aspergillus nidulans LO8030 expressing bgtABCD		Not Available

Chemical Taxonomy

Description

This compound belongs to the class of organic compounds known as branched fatty acids. These are fatty acids containing a branched chain.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acids and conjugates

Direct Parent

Branched fatty acids

Alternative Parents

Substituents

Branched fatty acid
Ketone
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

Not Available

Physical Properties

State

Not Available

Experimental Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Predicted Properties

Property	Value	Source
logP	2.99	ChemAxon
pKa (Strongest Acidic)	4.86	ChemAxon
pKa (Strongest Basic)	-7.4	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	3	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	54.37 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	71.84 m³·mol⁻¹	ChemAxon
Polarizability	29.22 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FoodDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

Not Available

Good Scents ID

Not Available

References

General References

Showing NP-Card for Bergamotene D (NP0333698)

MOL for NP0333698 (Bergamotene D)

3D MOL for NP0333698 (Bergamotene D)

3D SDF for NP0333698 (Bergamotene D)

3D-SDF for NP0333698 (Bergamotene D)

PDB for NP0333698 (Bergamotene D)

3D PDB for NP0333698 (Bergamotene D)

SMILES for NP0333698 (Bergamotene D)

INCHI for NP0333698 (Bergamotene D)

Structure for NP0333698 (Bergamotene D)

3D Structure for NP0333698 (Bergamotene D)